DNA is an underrepresented target for small molecule therapeutic agents. One reason for the dearth of DNA targeted drugs is that the fundamental molecular mechanisms that govern sequence- and structural-selective ligands to DNA remain poorly understood. In order to develop design principles for targeting specific DNA sites, a thorough understanding of the binding mechanisms of existing compounds that bind to DNA with unique types of selectivity is needed. The long-range goal of this project is to understand the mechanism of DNA intercalation reactions, with particular emphasis on the energetic basis of sequence- and structural-selective binding. Renewal is sought for a successful and highly productive basic science program that has produced several promising avenues for DNA-targeted drug development. Four-stranded G-quadruplex DNA structures have emerged as important functional elements within the genome, and represent important new targets for therapeutic drugs. G-quadruplexes are functional elements that are important in telomere biology, and are emerging as important control elements in the expression of many genes, particularly oncogenes. Research in the next funding period will focus on biophysical studies of G-quadruplex structure, folding and stability, and on their selective interactions specific quadruplex structures with drug-like molecules. Specific aims include: 1. Determination of the structure of the 200 nt single-stranded DNA overhang that is a conserved feature of human telomeres. 2. Determination of the thermodynamic stability of higher-order quadruplex structures and the kinetics of the folding. 3. Determination of the thermodynamics and kinetics of drug binding to specific quadruplex structures, including the higher-order structures in telomeric DNA and the G-quadruplex "silencer" element found in the c-myc promoter. The results of these proposed studies will deepen our understanding of the structure and stability of functionally important G-quadruplexes, and will provide fundamental mechanistic information of use in the rational design of new small molecules to selectively target functionally important quadruplex structures. PUBLIC HEALTH RELEVANCE: G-quadruplexes are four-stranded DNA structures that are thought to be functionally import elements in the human genome. Quadruplexes have emerged as potential drug targets. The proposed project will use computational and biophysical methods to study the structure, stability, and drug binding of functionally significant quadruplex structures. The results will be of fundamental use for guiding the design of new drugs targeted toward quadruplexes.